Tanya Berger-Wolf

Jenna Kline, Kilian Meier, Vandita Shukla et al.

Animal ecology data collection using drones represents a substantial investment of time, expertise, and financial resources. Yet most existing datasets serve only a single research community, limiting interdisciplinary reuse. We propose a unified drone dataset standard, FAIR^2 Drones, that bridges ecology, robotics, and computer vision by building on existing FAIR and AI-ready data frameworks while adding essential platform metadata and annotation specifications. Our standard enables datasets to simultaneously support ecological analysis, robotics algorithm development, and computer vision benchmarking. We provide open-source validation tools, reference implementations, and multimodal extensions linking drone imagery with complementary sensors such as camera traps, GPS, and acoustics. By standardizing metadata across disciplines, this framework maximizes the scientific return on investment for costly field deployments and accelerates cross-domain collaboration in environmental monitoring.

Dipanjyoti Paul, Arpita Chowdhury, Xinqi Xiong et al. · microsoft-research

We present a novel usage of Transformers to make image classification interpretable. Unlike mainstream classifiers that wait until the last fully connected layer to incorporate class information to make predictions, we investigate a proactive approach, asking each class to search for itself in an image. We realize this idea via a Transformer encoder-decoder inspired by DEtection TRansformer (DETR). We learn "class-specific" queries (one for each class) as input to the decoder, enabling each class to localize its patterns in an image via cross-attention. We name our approach INterpretable TRansformer (INTR), which is fairly easy to implement and exhibits several compelling properties. We show that INTR intrinsically encourages each class to attend distinctively; the cross-attention weights thus provide a faithful interpretation of the prediction. Interestingly, via "multi-head" cross-attention, INTR could identify different "attributes" of a class, making it particularly suitable for fine-grained classification and analysis, which we demonstrate on eight datasets. Our code and pre-trained models are publicly accessible at the Imageomics Institute GitHub site: https://github.com/Imageomics/INTR.

Zheda Mai, Arpita Chowdhury, Ping Zhang et al. · microsoft-research

Fine-tuning is arguably the most straightforward way to tailor a pre-trained model (e.g., a foundation model) to downstream applications, but it also comes with the risk of losing valuable knowledge the model had learned in pre-training. For example, fine-tuning a pre-trained classifier capable of recognizing a large number of classes to master a subset of classes at hand is shown to drastically degrade the model's accuracy in the other classes it had previously learned. As such, it is hard to further use the fine-tuned model when it encounters classes beyond the fine-tuning data. In this paper, we systematically dissect the issue, aiming to answer the fundamental question, "What has been damaged in the fine-tuned model?" To our surprise, we find that the fine-tuned model neither forgets the relationship among the other classes nor degrades the features to recognize these classes. Instead, the fine-tuned model often produces more discriminative features for these other classes, even if they were missing during fine-tuning! {What really hurts the accuracy is the discrepant logit scales between the fine-tuning classes and the other classes}, implying that a simple post-processing calibration would bring back the pre-trained model's capability and at the same time unveil the feature improvement over all classes. We conduct an extensive empirical study to demonstrate the robustness of our findings and provide preliminary explanations underlying them, suggesting new directions for future theoretical analysis. Our code is available at https://github.com/OSU-MLB/Fine-Tuning-Is-Fine-If-Calibrated.

M. Maruf, Arka Daw, Kazi Sajeed Mehrab et al. · microsoft-research

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Samuel Stevens, Jiaman Wu, Matthew J Thompson et al. · microsoft-research

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks and find that BioCLIP consistently and substantially outperforms existing baselines (by 16% to 17% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. https://imageomics.github.io/bioclip has models, data and code.

Lily Xu, Esther Rolf, Sara Beery et al. · mit

In this white paper, we synthesize key points made during presentations and discussions from the AI-Assisted Decision Making for Conservation workshop, hosted by the Center for Research on Computation and Society at Harvard University on October 20-21, 2022. We identify key open research questions in resource allocation, planning, and interventions for biodiversity conservation, highlighting conservation challenges that not only require AI solutions, but also require novel methodological advances. In addition to providing a summary of the workshop talks and discussions, we hope this document serves as a call-to-action to orient the expansion of algorithmic decision-making approaches to prioritize real-world conservation challenges, through collaborative efforts of ecologists, conservation decision-makers, and AI researchers.

Cheng-Hao Tu, Hong-You Chen, Zheda Mai et al. · microsoft-research

We propose a learning problem involving adapting a pre-trained source model to the target domain for classifying all classes that appeared in the source data, using target data that covers only a partial label space. This problem is practical, as it is unrealistic for the target end-users to collect data for all classes prior to adaptation. However, it has received limited attention in the literature. To shed light on this issue, we construct benchmark datasets and conduct extensive experiments to uncover the inherent challenges. We found a dilemma -- on the one hand, adapting to the new target domain is important to claim better performance; on the other hand, we observe that preserving the classification accuracy of classes missing in the target adaptation data is highly challenging, let alone improving them. To tackle this, we identify two key directions: 1) disentangling domain gradients from classification gradients, and 2) preserving class relationships. We present several effective solutions that maintain the accuracy of the missing classes and enhance the overall performance, establishing solid baselines for holistic transfer of pre-trained models with partial target data.

Mohannad Elhamod, Mridul Khurana, Harish Babu Manogaran et al.

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Dongyao Zhu, Zhen Wang, Xi Xiao et al.

Latent visual reasoning involves visual evidence more directly in multimodal reasoning by inserting continuous latent tokens before textual generation. However, the necessity of these latent tokens at inference remains ambiguous. We show that replacing latent tokens with random noise or removing them completely causes little performance degradation across spatial reasoning benchmarks. Reinforcement learning further diminishes the latent generation behavior after post-training. These observations raise a central question: Is latent visual reasoning still meaningful? We argue that its value should be measured by how effectively latent tokens guide learning, rather than whether they persist as an inference-time format. Our analysis shows that latent reasoning is unevenly favorable across question types, yet hard task-level routing for applying latent generation is brittle. Motivated by these findings, we propose an attention-based reward that encourages generated latent tokens to interact with later text tokens during RL. This reward promotes latent utilization when the latent mode is activated while preserving the flexibility to use pure-text reasoning. Experiments show that our method improves performance across perception and visual reasoning benchmarks, even when latent tokens are rarely generated after post-training. Our results highlight that, without explicit expression at inference, latent visual reasoning can shape better visual grounding and more accurate textual reasoning in silence. Our code and trained models are publicly available at \href{https://github.com/ddydyd32/silent-lvr/tree/master}{GitHub} and \href{https://huggingface.co/collections/cornuHGF/silent-lvr}{Hugging Face}.

Mridul Khurana, Arka Daw, M. Maruf et al.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Kazi Sajeed Mehrab, M. Maruf, Arka Daw et al.

We introduce Fish-Visual Trait Analysis (Fish-Vista), the first organismal image dataset designed for the analysis of visual traits of aquatic species directly from images using problem formulations in computer vision. Fish-Vista contains 69,126 annotated images spanning 4,154 fish species, curated and organized to serve three downstream tasks of species classification, trait identification, and trait segmentation. Our work makes two key contributions. First, we perform a fully reproducible data processing pipeline to process images sourced from various museum collections. We annotate these images with carefully curated labels from biological databases and manual annotations to create an AI-ready dataset of visual traits, contributing to the advancement of AI in biodiversity science. Second, our proposed downstream tasks offer fertile grounds for novel computer vision research in addressing a variety of challenges such as long-tailed distributions, out-of-distribution generalization, learning with weak labels, explainable AI, and segmenting small objects. We benchmark the performance of several existing methods for our proposed tasks to expose future research opportunities in AI for biodiversity science problems involving visual traits.

Harish Babu Manogaran, M. Maruf, Arka Daw et al.

A grand challenge in biology is to discover evolutionary traits - features of organisms common to a group of species with a shared ancestor in the tree of life (also referred to as phylogenetic tree). With the growing availability of image repositories in biology, there is a tremendous opportunity to discover evolutionary traits directly from images in the form of a hierarchy of prototypes. However, current prototype-based methods are mostly designed to operate over a flat structure of classes and face several challenges in discovering hierarchical prototypes, including the issue of learning over-specific prototypes at internal nodes. To overcome these challenges, we introduce the framework of Hierarchy aligned Commonality through Prototypical Networks (HComP-Net). The key novelties in HComP-Net include a novel over-specificity loss to avoid learning over-specific prototypes, a novel discriminative loss to ensure prototypes at an internal node are absent in the contrasting set of species with different ancestry, and a novel masking module to allow for the exclusion of over-specific prototypes at higher levels of the tree without hampering classification performance. We empirically show that HComP-Net learns prototypes that are accurate, semantically consistent, and generalizable to unseen species in comparison to baselines.

Ziheng Zhang, Jianyang Gu, Arpita Chowdhury et al. · microsoft-research

Class activation map (CAM) has been widely used to highlight image regions that contribute to class predictions. Despite its simplicity and computational efficiency, CAM often struggles to identify discriminative regions that distinguish visually similar fine-grained classes. Prior efforts address this limitation by introducing more sophisticated explanation processes, but at the cost of extra complexity. In this paper, we propose Finer-CAM, a method that retains CAM's efficiency while achieving precise localization of discriminative regions. Our key insight is that the deficiency of CAM lies not in "how" it explains, but in "what" it explains. Specifically, previous methods attempt to identify all cues contributing to the target class's logit value, which inadvertently also activates regions predictive of visually similar classes. By explicitly comparing the target class with similar classes and spotting their differences, Finer-CAM suppresses features shared with other classes and emphasizes the unique, discriminative details of the target class. Finer-CAM is easy to implement, compatible with various CAM methods, and can be extended to multi-modal models for accurate localization of specific concepts. Additionally, Finer-CAM allows adjustable comparison strength, enabling users to selectively highlight coarse object contours or fine discriminative details. Quantitatively, we show that masking out the top 5% of activated pixels by Finer-CAM results in a larger relative confidence drop compared to baselines. The source code and demo are available at https://github.com/Imageomics/Finer-CAM.

Arpita Chowdhury, Dipanjyoti Paul, Zheda Mai et al. · microsoft-research

We present a simple approach to make pre-trained Vision Transformers (ViTs) interpretable for fine-grained analysis, aiming to identify and localize the traits that distinguish visually similar categories, such as bird species. Pre-trained ViTs, such as DINO, have demonstrated remarkable capabilities in extracting localized, discriminative features. However, saliency maps like Grad-CAM often fail to identify these traits, producing blurred, coarse heatmaps that highlight entire objects instead. We propose a novel approach, Prompt Class Attention Map (Prompt-CAM), to address this limitation. Prompt-CAM learns class-specific prompts for a pre-trained ViT and uses the corresponding outputs for classification. To correctly classify an image, the true-class prompt must attend to unique image patches not present in other classes' images (i.e., traits). As a result, the true class's multi-head attention maps reveal traits and their locations. Implementation-wise, Prompt-CAM is almost a ``free lunch,'' requiring only a modification to the prediction head of Visual Prompt Tuning (VPT). This makes Prompt-CAM easy to train and apply, in stark contrast to other interpretable methods that require designing specific models and training processes. Extensive empirical studies on a dozen datasets from various domains (e.g., birds, fishes, insects, fungi, flowers, food, and cars) validate the superior interpretation capability of Prompt-CAM. The source code and demo are available at https://github.com/Imageomics/Prompt_CAM.

Namrata Banerji, Tanya Berger-Wolf

Accurate multistep forecasting of node-level attributes on dynamic graphs is critical for applications ranging from financial trust networks to biological networks. Existing spatiotemporal graph neural networks typically assume a static adjacency matrix. In this work, we propose an end-to-end dynamic edge-biased spatiotemporal model that ingests a multi-dimensional timeseries of node attributes and a timeseries of adjacency matrices, to predict multiple future steps of node attributes. At each time step, our transformer-based model injects the given adjacency as an adaptable attention bias, allowing the model to focus on relevant neighbors as the graph evolves. We further deploy a masked node-time pretraining objective that primes the encoder to reconstruct missing features, and train with scheduled sampling and a horizon-weighted loss to mitigate compounding error over long horizons. Unlike prior work, our model accommodates dynamic graphs that vary across input samples, enabling forecasting in multi-system settings such as brain networks across different subjects, financial systems in different contexts, or evolving social systems. Empirical results demonstrate that our method consistently outperforms strong baselines on Root Mean Squared Error (RMSE) and Mean Absolute Error (MAE).

Jenna Kline, Maksim Kholiavchenko, Samuel Stevens et al.

A comprehensive understanding of animal behavior ecology depends on scalable approaches to quantify and interpret complex, multidimensional behavioral patterns. Traditional field observations are often limited in scope, time-consuming, and labor-intensive, hindering the assessment of behavioral responses across landscapes. To address this, we present kabr-tools (Kenyan Animal Behavior Recognition Tools), an open-source package for automated multi-species behavioral monitoring. This framework integrates drone-based video with machine learning systems to extract behavioral, social, and spatial metrics from wildlife footage. Our pipeline leverages object detection, tracking, and behavioral classification systems to generate key metrics, including time budgets, behavioral transitions, social interactions, habitat associations, and group composition dynamics. Compared to ground-based methods, drone-based observations significantly improved behavioral granularity, reducing visibility loss by 15% and capturing more transitions with higher accuracy and continuity. We validate kabr-tools through three case studies, analyzing 969 behavioral sequences, surpassing the capacity of traditional methods for data capture and annotation. We found that, like Plains zebras, vigilance in Grevy's zebras decreases with herd size, but, unlike Plains zebras, habitat has a negligible impact. Plains and Grevy's zebras exhibit strong behavioral inertia, with rare transitions to alert behaviors and observed spatial segregation between Grevy's zebras, Plains zebras, and giraffes in mixed-species herds. By enabling automated behavioral monitoring at scale, kabr-tools offers a powerful tool for ecosystem-wide studies, advancing conservation, biodiversity research, and ecological monitoring.

Silvia Zuffi, Angjoo Kanazawa, Tanya Berger-Wolf et al.

We present the first method to perform automatic 3D pose, shape and texture capture of animals from images acquired in-the-wild. In particular, we focus on the problem of capturing 3D information about Grevy's zebras from a collection of images. The Grevy's zebra is one of the most endangered species in Africa, with only a few thousand individuals left. Capturing the shape and pose of these animals can provide biologists and conservationists with information about animal health and behavior. In contrast to research on human pose, shape and texture estimation, training data for endangered species is limited, the animals are in complex natural scenes with occlusion, they are naturally camouflaged, travel in herds, and look similar to each other. To overcome these challenges, we integrate the recent SMAL animal model into a network-based regression pipeline, which we train end-to-end on synthetically generated images with pose, shape, and background variation. Going beyond state-of-the-art methods for human shape and pose estimation, our method learns a shape space for zebras during training. Learning such a shape space from images using only a photometric loss is novel, and the approach can be used to learn shape in other settings with limited 3D supervision. Moreover, we couple 3D pose and shape prediction with the task of texture synthesis, obtaining a full texture map of the animal from a single image. We show that the predicted texture map allows a novel per-instance unsupervised optimization over the network features. This method, SMALST (SMAL with learned Shape and Texture) goes beyond previous work, which assumed manual keypoints and/or segmentation, to regress directly from pixels to 3D animal shape, pose and texture. Code and data are available at https://github.com/silviazuffi/smalst.

Samuel Stevens, Wei-Lun Chao, Tanya Berger-Wolf et al. · microsoft-research

To truly understand vision models, we must not only interpret their learned features but also validate these interpretations through controlled experiments. Current approaches either provide interpretable features without the ability to test their causal influence, or enable model editing without interpretable controls. We present a unified framework using sparse autoencoders (SAEs) that bridges this gap, allowing us to discover human-interpretable visual features and precisely manipulate them to test hypotheses about model behavior. By applying our method to state-of-the-art vision models, we reveal key differences in the semantic abstractions learned by models with different pre-training objectives. We then demonstrate the practical usage of our framework through controlled interventions across multiple vision tasks. We show that SAEs can reliably identify and manipulate interpretable visual features without model re-training, providing a powerful tool for understanding and controlling vision model behavior. We provide code, demos and models on our project website: https://osu-nlp-group.github.io/SAE-V.

Jianyang Gu, Samuel Stevens, Elizabeth G Campolongo et al. · microsoft-research

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Lukas Picek, Timm Haucke, Lukáš Adam et al.

Recognizing individual animals over time is central to many ecological and conservation questions, including estimating abundance, survival, movement, and social structure. Recent advances in automated identification from images and even acoustic data suggest that this process could be greatly accelerated, yet their promise has not translated well into ecological practice. We argue that the main barrier is not the performance of the automated methods themselves, but a mismatch between how those methods are typically developed and evaluated, and how ecological data is actually collected, processed, reviewed, and used. Future progress, therefore, will depend less on algorithmic gains alone than on recognizing that the usefulness of automated identification is grounded in ecological context: it depends on what question is being asked, what data are available, and what kinds of mistakes matter. Only by centering these questions can we move toward automated identification of individuals that is not only accurate but also ecologically useful, transparent, and trustworthy.

Elizabeth G. Campolongo, Yuan-Tang Chou, Ekaterina Govorkova et al.

Scientific discoveries are often made by finding a pattern or object that was not predicted by the known rules of science. Oftentimes, these anomalous events or objects that do not conform to the norms are an indication that the rules of science governing the data are incomplete, and something new needs to be present to explain these unexpected outliers. The challenge of finding anomalies can be confounding since it requires codifying a complete knowledge of the known scientific behaviors and then projecting these known behaviors on the data to look for deviations. When utilizing machine learning, this presents a particular challenge since we require that the model not only understands scientific data perfectly but also recognizes when the data is inconsistent and out of the scope of its trained behavior. In this paper, we present three datasets aimed at developing machine learning-based anomaly detection for disparate scientific domains covering astrophysics, genomics, and polar science. We present the different datasets along with a scheme to make machine learning challenges around the three datasets findable, accessible, interoperable, and reusable (FAIR). Furthermore, we present an approach that generalizes to future machine learning challenges, enabling the possibility of large, more compute-intensive challenges that can ultimately lead to scientific discovery.

Alyson East, Elizabeth G. Campolongo, Luke Meyers et al.

1) Biological collections house millions of specimens with digital images increasingly available through open-access platforms. However, most imaging protocols were developed for human interpretation without considering automated analysis requirements. As computer vision applications revolutionize taxonomic identification and trait extraction, a critical gap exists between current digitization practices and computational analysis needs. This review provides the first comprehensive practical framework for optimizing biological specimen imaging for computer vision applications. 2) Through interdisciplinary collaboration between taxonomists, collection managers, ecologists, and computer scientists, we synthesized evidence-based recommendations addressing fundamental computer vision concepts and practical imaging considerations. We provide immediately actionable implementation guidance while identifying critical areas requiring community standards development. 3) Our framework encompasses ten interconnected considerations for optimizing image capture for computer vision-powered taxonomic identification and trait extraction. We translate these into practical implementation checklists, equipment selection guidelines, and a roadmap for community standards development including filename conventions, pixel density requirements, and cross-institutional protocols. 4)By bridging biological and computational disciplines, this approach unlocks automated analysis potential for millions of existing specimens and guides future digitization efforts toward unprecedented analytical capabilities.

Vardaan Pahuja, Weidi Luo, Yu Gu et al.

Camera traps are important tools in animal ecology for biodiversity monitoring and conservation. However, their practical application is limited by issues such as poor generalization to new and unseen locations. Images are typically associated with diverse forms of context, which may exist in different modalities. In this work, we exploit the structured context linked to camera trap images to boost out-of-distribution generalization for species classification tasks in camera traps. For instance, a picture of a wild animal could be linked to details about the time and place it was captured, as well as structured biological knowledge about the animal species. While often overlooked by existing studies, incorporating such context offers several potential benefits for better image understanding, such as addressing data scarcity and enhancing generalization. However, effectively incorporating such heterogeneous context into the visual domain is a challenging problem. To address this, we propose a novel framework that transforms species classification as link prediction in a multimodal knowledge graph (KG). This framework enables the seamless integration of diverse multimodal contexts for visual recognition. We apply this framework for out-of-distribution species classification on the iWildCam2020-WILDS and Snapshot Mountain Zebra datasets and achieve competitive performance with state-of-the-art approaches. Furthermore, our framework enhances sample efficiency for recognizing under-represented species.

Jenna Kline, Anirudh Potlapally, Bharath Pillai et al.

We present the first release of SmartWilds, a multimodal wildlife monitoring dataset. SmartWilds is a synchronized collection of drone imagery, camera trap photographs and videos, and bioacoustic recordings collected during summer 2025 at The Wilds safari park in Ohio. This dataset supports multimodal AI research for comprehensive environmental monitoring, addressing critical needs in endangered species research, conservation ecology, and habitat management. Our pilot deployment captured four days of synchronized monitoring across three modalities in a 220-acre pasture containing Pere David's deer, Sichuan takin, Przewalski's horses, as well as species native to Ohio. We provide a comparative analysis of sensor modality performance, demonstrating complementary strengths for landuse patterns, species detection, behavioral analysis, and habitat monitoring. This work establishes reproducible protocols for multimodal wildlife monitoring while contributing open datasets to advance conservation computer vision research. Future releases will include synchronized GPS tracking data from tagged individuals, citizen science data, and expanded temporal coverage across multiple seasons.

Kenya Andrews, Mesrob Ohannessian, Tanya Berger-Wolf

Motivated by COVID-19 vaccine allocation, where vulnerable subpopulations are simultaneously more impacted in terms of health and more disadvantaged in terms of access to the vaccine, we formalize and study the problem of resource allocation when there are inherent access differences that correlate with advantage and disadvantage. We identify reducing resource disparity as a key goal in this context and show its role as a proxy to more nuanced downstream impacts. We develop a concrete access model that helps quantify how a given allocation translates to resource flow for the advantaged vs. the disadvantaged, based on the access gap between them. We then provide a methodology for access-aware allocation. Intuitively, the resulting allocation leverages more vaccines in locations with higher vulnerable populations to mitigate the access gap and reduce overall disparity. Surprisingly, knowledge of the access gap is often not needed to perform access-aware allocation. To support this formalism, we provide empirical evidence for our access model and show that access-aware allocation can significantly reduce resource disparity and thus improve downstream outcomes. We demonstrate this at various scales, including at county, state, national, and global levels.

S M Rayeed, Mridul Khurana, Alyson East et al.

Despite the ecological significance of invertebrates, global trait databases remain heavily biased toward vertebrates and plants, limiting comprehensive ecological analyses of high-diversity groups like ground beetles. Ground beetles (Coleoptera: Carabidae) serve as critical bioindicators of ecosystem health, providing valuable insights into biodiversity shifts driven by environmental changes. While the National Ecological Observatory Network (NEON) maintains an extensive collection of carabid specimens from across the United States, these primarily exist as physical collections, restricting widespread research access and large-scale analysis. To address these gaps, we present a multimodal dataset digitizing over 13,200 NEON carabids from 30 sites spanning the continental US and Hawaii through high-resolution imaging, enabling broader access and computational analysis. The dataset includes digitally measured elytra length and width of each specimen, establishing a foundation for automated trait extraction using AI. Validated against manual measurements, our digital trait extraction achieves sub-millimeter precision, ensuring reliability for ecological and computational studies. By addressing invertebrate under-representation in trait databases, this work supports AI-driven tools for automated species identification and trait-based research, fostering advancements in biodiversity monitoring and conservation.

Luke Meyers, Anirudh Potlapally, Yuyan Chen et al.

Plant phenology, the study of cyclical events such as leafing out, flowering, or fruiting, has wide ecological impacts but is broadly understudied, especially in the tropics. Image analysis has greatly enhanced remote phenological monitoring, yet capturing phenology at the individual level remains challenging. In this project, we deployed low-cost, animal-triggered camera traps at the Pu'u Maka'ala Natural Area Reserve in Hawaii to simultaneously document shifts in plant phenology and flora-faunal interactions. Using a combination of foundation vision models and traditional computer vision methods, we measure phenological trends from images comparable to on-the-ground observations without relying on supervised learning techniques. These temporally fine-grained phenology measurements from camera-trap images uncover trends that coarser traditional sampling fails to detect. When combined with detailed visitation data detected from images, these trends can begin to elucidate drivers of both plant phenology and animal ecology.

Samuel Stevens, Jacob Beattie, Tanya Berger-Wolf et al.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Ziheng Zhang, Xinyue Ma, Arpita Chowdhury et al.

This work investigates descriptive captions as an additional source of supervision for biological multimodal foundation models. Images and captions can be viewed as complementary samples from the latent morphospace of a species, each capturing certain biological traits. Incorporating captions during training encourages alignment with this shared latent structure, emphasizing potentially diagnostic characters while suppressing spurious correlations. The main challenge, however, lies in obtaining faithful, instance-specific captions at scale. This requirement has limited the utilization of natural language supervision in organismal biology compared with many other scientific domains. We complement this gap by generating synthetic captions with multimodal large language models (MLLMs), guided by Wikipedia-derived visual information and taxon-tailored format examples. These domain-specific contexts help reduce hallucination and yield accurate, instance-based descriptive captions. Using these captions, we train BioCAP (i.e., BioCLIP with Captions), a biological foundation model that captures rich semantics and achieves strong performance in species classification and text-image retrieval. These results demonstrate the value of descriptive captions beyond labels in bridging biological images with multimodal foundation models.

Zhenyang Feng, Zihe Wang, Jianyang Gu et al.

We study image segmentation in the biological domain, particularly trait segmentation from specimen images (e.g., butterfly wing stripes, beetle elytra). This fine-grained task is crucial for understanding the biology of organisms, but it traditionally requires manually annotating segmentation masks for hundreds of images per species, making it highly labor-intensive. To address this challenge, we propose a label-efficient approach, Static Segmentation by Tracking (SST), based on a key insight: while specimens of the same species exhibit natural variation, the traits of interest show up consistently. This motivates us to concatenate specimen images into a ``pseudo-video'' and reframe trait segmentation as a tracking problem. Specifically, SST generates masks for unlabeled images by propagating annotated or predicted masks from the ``pseudo-preceding'' images. Built upon recent video segmentation models, such as Segment Anything Model 2, SST achieves high-quality trait segmentation with only one labeled image per species, marking a breakthrough in specimen image analysis. To further enhance segmentation quality, we introduce a cycle-consistent loss for fine-tuning, again requiring only one labeled image. Additionally, we demonstrate the broader potential of SST, including one-shot instance segmentation in natural images and trait-based image retrieval.

Devis Tuia, Benjamin Kellenberger, Sara Beery et al.

Data acquisition in animal ecology is rapidly accelerating due to inexpensive and accessible sensors such as smartphones, drones, satellites, audio recorders and bio-logging devices. These new technologies and the data they generate hold great potential for large-scale environmental monitoring and understanding, but are limited by current data processing approaches which are inefficient in how they ingest, digest, and distill data into relevant information. We argue that machine learning, and especially deep learning approaches, can meet this analytic challenge to enhance our understanding, monitoring capacity, and conservation of wildlife species. Incorporating machine learning into ecological workflows could improve inputs for population and behavior models and eventually lead to integrated hybrid modeling tools, with ecological models acting as constraints for machine learning models and the latter providing data-supported insights. In essence, by combining new machine learning approaches with ecological domain knowledge, animal ecologists can capitalize on the abundance of data generated by modern sensor technologies in order to reliably estimate population abundances, study animal behavior and mitigate human/wildlife conflicts. To succeed, this approach will require close collaboration and cross-disciplinary education between the computer science and animal ecology communities in order to ensure the quality of machine learning approaches and train a new generation of data scientists in ecology and conservation.

Moniba Keymanesh, Tanya Berger-Wolf, Micha Elsner et al.

In consequential domains such as recidivism prediction, facility inspection, and benefit assignment, it's important for individuals to know the decision-relevant information for the model's prediction. In addition, predictions should be fair both in terms of the outcome and the justification of the outcome. In other words, decision-relevant features should provide sufficient information for the predicted outcome and should be independent of the membership of individuals in protected groups such as race and gender. In this work, we focus on the problem of (un)fairness in the justification of the text-based neural models. We tie the explanatory power of the model to fairness in the outcome and propose a fairness-aware summarization mechanism to detect and counteract the bias in such models. Given a potentially biased natural language explanation for a decision, we use a multi-task neural model and an attribution mechanism based on integrated gradients to extract high-utility and low-bias justifications in form of a summary. The extracted summary is then used for training a model to make decisions for individuals. Results on several real world datasets suggest that our method drastically limits the demographic leakage in the input (fairness in justification) while moderately enhancing the fairness in the outcome. Our model is also effective in detecting and counteracting several types of data poisoning attacks that synthesize race-coded reasoning or irrelevant justifications.

Shishir Adhikari, Akshay Uppal, Robin Mermelstein et al.

Cannabis legalization has been welcomed by many U.S. states but its role in escalation from tobacco e-cigarette use to cannabis vaping is unclear. Meanwhile, cannabis vaping has been associated with new lung diseases and rising adolescent use. To understand the impact of cannabis legalization on escalation, we design an observational study to estimate the causal effect of recreational cannabis legalization on the development of pro-cannabis attitude for e-cigarette users. We collect and analyze Twitter data which contains opinions about cannabis and JUUL, a very popular e-cigarette brand. We use weakly supervised learning for personal tweet filtering and classification for stance detection. We discover that recreational cannabis legalization policy has an effect on increased development of pro-cannabis attitudes for users already in favor of e-cigarettes.

Lea A. Shanley, Lucy Fortson, Tanya Berger-Wolf et al.

Machine learning, artificial intelligence, and deep learning have advanced significantly over the past decade. Nonetheless, humans possess unique abilities such as creativity, intuition, context and abstraction, analytic problem solving, and detecting unusual events. To successfully tackle pressing scientific and societal challenges, we need the complementary capabilities of both humans and machines. The Federal Government could accelerate its priorities on multiple fronts through judicious integration of citizen science and crowdsourcing with artificial intelligence (AI), Internet of Things (IoT), and cloud strategies.

Chainarong Amornbunchornvej, Elena Zheleva, Tanya Berger-Wolf

Granger causality is a fundamental technique for causal inference in time series data, commonly used in the social and biological sciences. Typical operationalizations of Granger causality make a strong assumption that every time point of the effect time series is influenced by a combination of other time series with a fixed time delay. The assumption of fixed time delay also exists in Transfer Entropy, which is considered to be a non-linear version of Granger causality. However, the assumption of the fixed time delay does not hold in many applications, such as collective behavior, financial markets, and many natural phenomena. To address this issue, we develop Variable-lag Granger causality and Variable-lag Transfer Entropy, generalizations of both Granger causality and Transfer Entropy that relax the assumption of the fixed time delay and allow causes to influence effects with arbitrary time delays. In addition, we propose methods for inferring both variable-lag Granger causality and Transfer Entropy relations. In our approaches, we utilize an optimal warping path of Dynamic Time Warping (DTW) to infer variable-lag causal relations. We demonstrate our approaches on an application for studying coordinated collective behavior and other real-world casual-inference datasets and show that our proposed approaches perform better than several existing methods in both simulated and real-world datasets. Our approaches can be applied in any domain of time series analysis. The software of this work is available in the R-CRAN package: VLTimeCausality.

Chainarong Amornbunchornvej, Tanya Berger-Wolf

How do groups of individuals achieve consensus in movement decisions? Do individuals follow their friends, the one predetermined leader, or whomever just happens to be nearby? To address these questions computationally, we formalize "Coordination Strategy Inference Problem". In this setting, a group of multiple individuals moves in a coordinated manner towards a target path. Each individual uses a specific strategy to follow others (e.g. nearest neighbors, pre-defined leaders, preferred friends). Given a set of time series that includes coordinated movement and a set of candidate strategies as inputs, we provide the first methodology (to the best of our knowledge) to infer whether each individual uses local-agreement-system or dictatorship-like strategy to achieve movement coordination at the group level. We evaluate and demonstrate the performance of the proposed framework by predicting the direction of movement of an individual in a group in both simulated datasets as well as two real-world datasets: a school of fish and a troop of baboons. Moreover, since there is no prior methodology for inferring individual-level strategies, we compare our framework with the state-of-the-art approach for the task of classification of group-level-coordination models. The results show that our approach is highly accurate in inferring the correct strategy in simulated datasets even in complicated mixed strategy settings, which no existing method can infer. In the task of classification of group-level-coordination models, our framework performs better than the state-of-the-art approach in all datasets. Animal data experiments show that fish, as expected, follow their neighbors, while baboons have a preference to follow specific individuals. Our methodology generalizes to arbitrary time series data of real numbers, beyond movement data.

Matteo Foglio, Lorenzo Semeria, Guido Muscioni et al.

We are losing biodiversity at an unprecedented scale and in many cases, we do not even know the basic data for the species. Traditional methods for wildlife monitoring are inadequate. Development of new computer vision tools enables the use of images as the source of information about wildlife. Social media is the rich source of wildlife images, which come with a huge bias, thus thwarting traditional population size estimate approaches. Here, we present a new framework to take into account the social media bias when using this data source to provide wildlife population size estimates. We show that, surprisingly, this is a learnable and potentially solvable problem.

Guido Muscioni, Riccardo Pressiani, Matteo Foglio et al.

Activity recognition and, more generally, behavior inference tasks are gaining a lot of interest. Much of it is work in the context of human behavior. New available tracking technologies for wild animals are generating datasets that indirectly may provide information about animal behavior. In this work, we propose a method for classifying these data into behavioral annotation, particularly collective behavior of a social group. Our method is based on sequence analysis with a direct encoding of the interactions of a group of wild animals. We evaluate our approach on a real world dataset, showing significant accuracy improvements over baseline methods.